ChangeLog

2018-05-01  George G. Vega Yon <g.vegayon@gmail.com>

	* R/pies.r: All dependencies have been moved to polygons.
	* R/predict.r: idem.


2018-04-17  George G. Vega Yon <g.vegayon@gmail.com>

	* src/phylo.cpp: Removed prediction functions (wrongly implemented).
	* R/predict-bis.r: Documenting posterior probabilities.
	* R/predict.r: Updating predict methods to use the correct version of
	  the posterior probabilities.
	* tests/testthat/test-predict.r: Adding new tests.


2018-04-11  George G. Vega Yon <g.vegayon@gmail.com>

	* src/predict.cpp: New function implementing posterior probabilities.
	  Now we are using pre-order to compute such probs (see paper).
	* R/predict-bis.r: Idem. Including a brute-force version intended
	  to be used for testing.

	* src/*: Fixing iter++ to ++iter when necesary (an bad practice that
	  now warns when compiling).


2018-02-28  George G. Vega Yon <g.vegayon@gmail.com>

	* tests/*: Adding test checking that likelihood in model with eta = 
	  1/2 is proportional to the likelihood without etas.


2018-02-27  George G. Vega Yon <g.vegayon@gmail.com>

	* src/phylo.cpp: Updating etas in the model. Now it is the probability
	  of not reporting a discovery given the observed state (before it was
	  the true state).
	* src/sim_phylo.cpp: idem.
	* tests/*: idem.


2018-02-22  George G. Vega Yon <g.vegayon@gmail.com>

	* src/phylo.cpp: Fixing 'error' back.

	* R/predict.r: Adding eta to the call.
	* R/plot_loglike.r: idem.
	* R/estimation.r: idem, and adding function to try to compute inv.

	* tests/testthat/*.r: Adding eta to the tests.


2018-02-21  George G. Vega Yon <g.vegayon@gmail.com>

	* src/phylo.cpp: Adding the eta parameter for controlling for
	annotation bias.
	* src/sim_phylo.cpp: Idem.
	* R/estimation.r: Idem.
	* R/simulation.r: Idem.
	* R/plot_loglike.r: Idem.
	* R/loglike.r: Idem.


2018-01-25  George G. Vega Yon <g.vegayon@gmail.com>

	* R/simulation.r: Values of `informative` and `maxtries` were not
	passed
	  to simulate_fun_on_tree.


2018-01-18  George G. Vega Yon <g.vegayon@gmail.com>

	* R/estimation.r: Fixing checking of non-informative data.

	* R/predict.r: Indexing of edges was wrong.
	* src/phylo.cpp: predict_fun was taking the wrong id for root node.
	  Also, when the node was the rootnode, d0i should yield probabilities
	  equal to pi.

	* R/data-management.r: Removing functions that are no longer required.
	* src/tree.cpp: Idem.

	* tests/testthat/test-data-management.r: New set of tests.


2018-01-11  George G. Vega Yon <g.vegayon@gmail.com>
	
	* R/ape.r: Fixing case in which as.phylo.matrix processes a tree with
	  only leafs and a root.

	* R/data-management.r: Fixing bug in plot.aphylo.


2018-01-10  George G. Vega Yon <g.vegayon@gmail.com>

	* R/estimation.r: Doc + estimation checks whether aphylo is informative.

	* R/prune.r: Completely removed. No longer needed.

	* R/simulation.r: Working on Doc + sim functions check if the resulting
	  tree is informative or not + new function rdrop_annotations.
	* tests/testthat/*: Several new tests on the previous point.


2018-01-09  George G. Vega Yon <g.vegayon@gmail.com>

	* R/ape.r: Working on documentation.
	* R/data-management.r: idem
	* R/simulation.r: idem.

	* R/predict.r: Adapting pred functions to new structure of aphylo.
	

2018-01-04  George G. Vega Yon <g.vegayon@gmail.com>

	* src/misc.cpp: New function reduce_pseq proposes a peeling seq that
	  skips ininformative nodes.

	* R/data-management.r: Remove a bunch of routines that wont be used
	  anymore related to PO trees.


2018-01-03  George G. Vega Yon <g.vegayon@gmail.com>

	* src/sim_phylo.cpp: Simulating trees using ape's phylo convention. 
	  about 20x faster than rtree. Returns a phylo object.
	* R/simulation.r: Idem.

	* src/tree.cpp: Function to list offspring of a tree.
	* R/data-management.r: idem.

	* src/phylo.cpp: Likelihood was not been computed at the root node!
	  but this is for the new method. The old one was OK.
	* 

2017-12-20  George G. Vega Yon <g.vegayon@gmail.com>

	* playground/*: Working on functions to prune trees using po traversal
	  or pre-order traversal. Algorithms working and good exercise to have
	  a better understanding of the pruning algorithm.


2017-10-18  George G. Vega Yon <g.vegayon@gmail.com>
	* R/data-management.r: Fixing bug in plot.aphylo.

	* playground/presentations: Working on EAC presentation.


2017-10-04  George G. Vega Yon <g.vegayon@gmail.com>
	* R/data-management.r: Working in a standard method to point to 
	  nodes ids.
	* R/predict.r: Idem.

	* R/prune.r: New example prunning leafs.


2017-10-03  George G. Vega Yon <g.vegayon@gmail.com>
	* R/data-management.r: New constructor method for class po_tree.
	  Now it also includes branch lengths.

	* R/simulation.r: Move documentation of sim_tree.
	
	* src/sim_tree.cpp: Efficiency.
	* src/tree.cpp: Change sorting in final edgelist.	


2017-09-28  George G. Vega Yon <g.vegayon@gmail.com>
	* R/data-management.r: Removing names for the po_tree labels.

	* R/prune.r: New (a bit complex) function to prune trees.


2017-09-07  George G. Vega Yon <g.vegayon@gmail.com>
	* R/data-management.r: leafs now has its own manual, plus
	  new internal checks checking labels.

	* src/phylo.cpp: -noffspring- removed since now we use Rf_length.
	  This included changes in all the functions that used that argument.

	* R/simulation.r: po_tree now has the labels as attributes, including
	  the offspring.
	* src/sim_phylo.cpp: sim_tree now returns an integer matrix (edgelist).
	  Only offspring and labels are included as attributes. 


2017-09-07  George G. Vega Yon <g.vegayon@gmail.com>
	* R/panther.r: Now the user can choose which one to use.

	* playground/ape_now_supports_singletons*: A small benchmark between
	  rncl and ape.


2017-09-05  George G. Vega Yon <g.vegayon@gmail.com>
	* R/panther.r: Now using nrcl to read newick

2017-08-31  George G. Vega Yon <g.vegayon@gmail.com>
	* R/pies.r: New function to rescale y-coords so that aspect ratio
	  is kept.

2017-08-29  George G. Vega Yon <g.vegayon@gmail.com>
	* R/panther.r: Capturing info from newick extended version.
	* R/pies.r: Adding more features to the pieplot.
	* R/predict.r: New plot method for prediction.
	
	* configure.ac: Compaling using OpenMP.
	* condigure: idem.
	* src/Makevars.in: idem.


2017-08-04  George G. Vega Yon <g.vegayon@gmail.com>
	* R/panther.r: New function to read panther trees' annotation.


2017-08-01  George G. Vega Yon <g.vegayon@gmail.com>
	* R/data-management.r: Working on aphylo-class. Plot method
	  using ggtree.
	* R/estimation.r: Removing ABC method and cleaning code.
	* tests/*: Adding more tests.


2017-07-31  George G. Vega Yon <g.vegayon@gmail.com>
	* Overall, working on the -aphylo- class object. Now it is better
	  integrated with ape-phylo objects. Also, including class checks
	  for the class creation method.

2017-07-12  George G. Vega Yon <g.vegayon@gmail.com>
	* playground/simulations: Moved to a different project aphylo_paper.
	* src/phylo.cpp: Changed Pi to be -double- no longer an -arma::mat-.
	* R/mle.r, R/plog_loglike.r: Idem.
	* tests/testthat/test-loglikelihood.r: Idem.


2017-07-11  George G. Vega Yon <g.vegayon@gmail.com>
	* src/quality.cpp, R/predict.r: Included new function to compute
	  expected value of random imputation given parameter alpha.


2017-05-31  George G. Vega Yon <g.vegayon@gmail.com>
	* R/simulations.r: Fixed a small bug related to names of a vector.


2017-05-02  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mle.r: Added new functions to predict and evaluate prediction.
	  Plus, some code improvement.
	* R/plot_loglike.r: Making code more clear.
	* src/phylo.cpp: Prediction functions.
	* src/misc.cpp: Function to compute geodesics.
	* vignettes/*: Working on doc, including data imputation.


2017-04-19  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mle.r: Using fnscale and parscale in optim and abc_optim.
	  Now the functions maximize so its all out of the box.


2017-04-18  George G. Vega Yon <g.vegayon@gmail.com>
	* *: Moved the MCMC to a new project: USCbiostats/amcmc


2017-04-13  George G. Vega Yon <g.vegayon@gmail.com>
	* R/data-management.r: Functions as.phylo and recode_vertices
	  rewritten and renamed to as.apephylo and as_ape_tree. Also
	  now all use an edgelist instead of offspring and parent vectors.
	* src/phylo.cpp: Changing name from Z to annotations (makes more sense).
	* R/mle.r: Idem.
	* src/sim_phylo.cpp: Name conventions, again, now edgelists are always
	  in the form of (parent, offspring).
	* src/tree.cpp: Function to relabel edgelist so that these form a
	  partial ordered tree. Plus more doc.


2017-04-12  George G. Vega Yon <g.vegayon@gmail.com>
	* src/tree: New functions for recoding trees as PO.
	* R/*: Changing language... now phylo_tree is aphylo (Annotated
	  phylogenetic tree).
	* R/data-management.r: get_offspring changed to new_aphylo, and
	  now includes more checks on the edge and annotations.


2017-03-29  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mcmc.r: Moved phylo_mcmc to R/mle.r
	* R/mle.r: MLE now uses stats::optim rather than own NR.
	* tests/testthat/*: new tests

2017-03-22  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mcmc.r: Multiple parallel chains and passing extra arguments to
	fun.
	* R/mle.r: Working on printing method.
	* R/simulation.r: Adding templates for doc.
	* tests/*: Adding more tests.
	* src/phylo.cpp: Cleaning code and collapsing prob loops.


2017-03-08  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mle.r: New print method + covar matrix in phylo_mle.


2017-03-07  George G. Vega Yon <g.vegayon@gmail.com>
	* R/data-management.r: Working with -as.phylo- method.
	* src/sim_phylo.cpp: Moving the sim_tree function there.
	* src/sim_tree.cpp: . .
	* playground/simulating_and_estimating_data.r: Check the performance
	  of the mle estimator.
	* R/simulation.r: Implements the function for sim annotated phylo
	  trees.
	* tests/testthat/test-data-management.r: New set of tests


2017-02-28  George G. Vega Yon <g.vegayon@gmail.com>
	* src/sim_tree.cpp: A function to simulate Directed Acyclic Graphs
	  is faster than ape::rtree and more convenient since it creates
	  the labelling that we require.


2017-02-23  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mcmc.r: -scale- now a vector. New example using MVN dist.
	* src/mcmc.cpp: idem.
	* src/sim_phylo.cpp: Multiple functions can be generated at the time.
	* vignettes/*: Just doing some cleaning.

2017-02-22  George G. Vega Yon <g.vegayon@gmail.com>
	* R/data-management.r: -as.phylo- method for -phylo_offspring-,
	  and removed igraph links (replaced by -ape-).
	* playground/FormatTreeR_24Oct2012.pdf: Formally describes
	  the phylo objects.
	* src/sim_phylo.cpp: Function to simulate phylo trees.


2017-02-16  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mcmc.r: Fixing small bug in output.
	* R/mle.r: Adding an example with MCMC and improving doc.
	* playground/*.r: Some tests of the performance of MCMC
	  including speed comparisons against the mcmc::metrop
	  function.


2017-02-15  George G. Vega Yon <g.vegayon@gmail.com>
	* src/mcmc_misc.cpp -> src/mcmc.cpp: New version of the mcmc
	  algorithm implemented using Rcpp.
	* R/mcmc.r: New option -useCpp- allows using a C++ version
	  of the algorithm. Speed improvement of ~ 50%.
	* R/mle.r: Working on documentation for the phylo_mcmc
	  function.
	* playground/mcmc_benchmark...: Measuring speed gains
	  of new MCMC implementation.


2017-02-14  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mcmc.r: mcmc now is MCMC and returns an object of class mcmc
	  from the coda R package. Also, new argument -thin- allows
	  'thinning' the samples to reduce autocorrelation between
	  draws. Also, working on aperiodicity of MCMC.

2017-02-09  George G. Vega Yon <g.vegayon@gmail.com>
	* src/mcmc_misc.cpp: Started to write Gibbs Sampler.


2017-02-03  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mcmc.r: Adding example and fixing travis (doc missing). Also
	  including check of -ub- and -lb- parameters.
	* tests/testthat/test-mcmc.r: New test for MCMC.


2017-02-02  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mle.r: Improving doc. Now optim pars are passed via `control`.
	  mcmc using own method.
	* src/mcmc_misc.cpp, R/mcmc.r: New function for implemting MCMC
	  with hastings ratio.
	  

2017-02-01  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mle.r: Adding more examples (filling zeros), plus more tunning
	  options for the NR method.


2017-01-18  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mle.r, R/plot_loglike.r: Changing coding style.
	* R/mle.r: Working on NR (now gives more reasonable ans
	  and identical to ABCoptim).
	* src/phylo.cpp: leaf_prob can be computed faster now,
	  and gain_loss_prob changed to prob_mat.
	* src/phylo.h: Adding header.
	* tests/testthat/*.r: leaf_prob now uses mu instead of M.


2017-01-18  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mle.r: Improving doc + output (class) structure.
	* R/phylogenetic.r: Adding more imports + doc data.
	* test/testthat/*: Adding tests (making sure the ll works).
	* readme.rmd: Adding code coverage, travis and appveyor.
	* src/peeling_cpp.cpp: Improving documentation.


2017-01-11  George G. Vega Yon <g.vegayon@gmail.com>
	* R/mle.r: Maximum Likelihood estimation function and methods.
	* R/phylogenetic.r: Adding package requirements for MLE.


2017-01-11  George G. Vega Yon <g.vegayon@gmail.com>
	* R/data-management.r: get_offspring now returns neat experiment
	* R/plot_loglike.r: Fixed bug
	* playground/example.r: Accomodating script to changes in
	get_offspring
	* playground/root_node_prob.rmd: Notes on root node.


2017-01-10  George G. Vega Yon <g.vegayon@gmail.com>
	* R/data-management.r: Changing offsprings to offspring
	* R/methods.r: Idem.
	* R/phylogenetic.r: Adding new imports.
	* playground/example.r: Fixing N-R optim.
	* vignettes/phylogenetic_trees.rmd: Working on doc.
	* src/peeling_rcpp.cpp: Adding beta dist prior for psi, and,
	  fixing bug on leaf probabilities.
	* R/plot_loglike.r: New function to visualize LogLike.


2017-01-03  George G. Vega Yon <g.vegayon@gmail.com>
	* R/data-management.r: Now experimental data is filled. and
	  adding new set of functions.
	* vignettes/phylogemetic_trees.rmd: Working on doc.


2017-01-03  George G. Vega Yon <g.vegayon@gmail.com>
	* data/*: Adding data more neatly.
	* R/*.r: Adding new methods for printing and preparing data.
	* vignettes/*: Using html_vignette output.


2016-12-20  George G. Vega Yon <g.vegayon@gmail.com>
	* Initial commit.